chr11-112806159-C-A

Variant names:

• chr11-112806159-C-A
• rs685478

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.471 in 151,842 control chromosomes in the GnomAD database, including 17,506 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71372 AN: 151724 Hom.: 17466 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.461

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.471 AC: 71468 AN: 151842 Hom.: 17506 Cov.: 31 AF XY: 0.478 AC XY: 35456 AN XY: 74182

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.463

Alfa AF: 0.366 Hom.: 1644

Bravo AF: 0.477

Asia WGS AF: 0.621 AC: 2161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs685478; hg19: chr11-112676882;